Water Depth: Of particular interest in any study of ancient marine environments is the issue of water depth, because depth is correlated with many other variables (e.g. temperature, light, environmental energy) that have a strong controlling influence on benthic (bottom dwelling) organisms. Unfortunately, depth is also a difficult parameter to assess, as there is little direct information on water depth. The Rochester Shale shows abundant evidence of deeper storm wave-current deposited sediments. These include thin (1 to 10 cm) tabular calcisiltite beds that show sharp soles with tool marks and scours, micrograding, planar to small scale hummocky cross stratification, all indicators of deposition from gradient currents and/or combined flows that involve minor wave action. These deposits of silt-sized carbonate sediment were swept into the muddy basin during times of strong backflow currents or gradient currents. This places the seafloor within the reach of storm-generated currents and the presence of hummocks suggests interference of wave effects. These silty beds were probably deposited toward the deeper end of storm wave-current effects, i.e., at deep storm wave base. For shallow interior seas this position may have been as much as 50 meters (~150 feet) or slightly more but clearly the seafloor was not in very great depths. Very gentle distal ends of gradient currents may have reoriented and aligned the carcasses of trilobites such as Dalmanites into "windrows." Certain mass occurrences of Dalmanites show preferred orientations. However, the currents were not strong enough to impart a very strong preferred orientation. In shallower depths, storm waves locally broke up colonies of bryozoans and shells and reworked them into local lenses of slightly broken debris.

Shallower water sediments are indicated in some of the higher Lockport Group above the Rochester Formation. For example, the Gasport Limestone that occurs above the Rochester Shale shows bimodal or herringbone cross bedded crinoidal sand and gravel; such evidence indicates deposition in water shallow enough to be affected by strong, reversing tidal currents, probably no more than 10 to 15 meters of water. These beds also contain locally abundant colonial corals and stromatoporoid sponges that probably required shallow, well-lit waters. Rochester sediments accumulated in considerably deeper water.

Light intensity: Evidence for ancient light levels is more tentative. Small mounds or bioherms at the top of the Irondequoit Limestone that protrude upward into the Rochester Shale are composed of clotted lime mud or micrite, as well as leaf-like Lichenalia bryozoans. The clotted muds resemble thrombolites produced by the blue-green cyanobacterium Girvanella, though more detailed study is needed. These structures thus imply a position within the euphotic (well-lit zone) at least for the basal transition into the Rochester Shale. If the forms, such as Inocaulis (Figures 120 - 122) are actually green algae and not dendroid graptolites then these would also imply a position in the euphotic zone. Certain units yielding assemblages of brachiopods similar to those of the Rochester Shale, such as those in the Silurian of Gotland, have yielded abundant microborings of algae and cyanobacteria ("blue green" bacteria). Since these organisms require light for photosynthesis they provide evidence for deposition in the photic zone (Glaub and Bundeschuh, 1997; Glaub et al., 2007). However, Rochester fossils have not yielded these sorts of traces to date. The presence of relatively sophisticated schizochroal (multi-faceted, with discrete, non-distorting lenses) turreted eyes in the abundant trilobite Dalmanites points to the presence of some light, as organisms living in perpetually dark settings (such as cave crayfish) tend to have weak or non-existent eyes. Eyes of dalmanitids were adapted for forming clear images and this requires sufficient light. The large size of the eyes, on the other hand may indicate relatively low light levels to which the organisms were adapted. Given that the Rochester seafloor was no doubt muddy and prone to high turbidity this indicates depths of just a few tens of meters. Together these lines of evidence suggest deposition in the dysphotic to lower euphotic zone, at depths of perhaps 30 to 60 meters of water, shallowest to the north where the Rochester Shale pinched out into carbonate shoals with sediments resembling the Irondequoit Limestone and deeper to the south where Rochester facies were mainly dark, barren shales, reflecting stagnant, dysoxic environments.